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AMEN: v.1.1.2 released, four changes & three bugs fixed !
07-25-2008
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Bio::Annotation::Tree(3pm) User Contributed Perl Documentation Bio::Annotation::Tree(3pm) NAME
Bio::Annotation::Tree - Provide a tree as an annotation to a Bio::AnnotatableI object SYNOPSIS
# Read a tree and an alignment $treeio=Bio::TreeIO->new(-file=>'foo.dnd', -format=>'newic'); $tree=$treeio->next_tree; $alnio=Bio::AlignIO->new(-file=>'foo.aln', -format=>'clustalw'); $aln=$alnio->next_aln; # Construct a tree annotation $ann_tree = Bio::Annotation::Tree->new (-tree_id => 'mytree', -tree_obj => $tree, ); # Add the tree annotation to AlignI $ac = Bio::Annotation::Collection->new(); $ac->add_Annotation('tree', $ann_tree); $aln->annotation($ac); # NOTE & TODO: # The above procedures are sensible only if # the tree is generated from the alignment. However, # currently no effort has been made to check the consistency # between the tree OTU names and the sequence names DESCRIPTION
Provides a Bio::AnnotationI object which contains a Bio::Tree::TreeI, which can be added to a Bio::AnnotationCollectionI, which in turn be attached to a Bio::AnnotatableI (typically a Bio::AlignI object) AUTHOR
Weigang Qiu - weigang at genectr.hunter.cuny.edu CONTRIBUTORS
Aaron Mackey Jason Stajich APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a '_' AnnotationI implementing functions as_text Title : as_text Usage : $ann_tree->as_text(); Function: output tree as a string Returns : a newic tree file Args : None display_text Title : display_text Usage : my $str = $ann->display_text(); Function: returns a string. Unlike as_text(), this method returns a string formatted as would be expected for te specific implementation. One can pass a callback as an argument which allows custom text generation; the callback is passed the current instance and any text returned Example : Returns : a string Args : [optional] callback hash_tree Title : hash_tree Usage : my $hashtree = $value->hash_tree Function: For supporting the AnnotationI interface just returns the value as a hashref with the key 'value' pointing to the value Returns : hashrf to tree Args : none tagname Title : tagname Usage : $obj->tagname($newval) Function: Get/set the tagname for this annotation value. Setting this is optional. If set, it obviates the need to provide a tag to Bio::AnnotationCollectionI when adding this object. When obtaining an AnnotationI object from the collection, the collection will set the value to the tag under which it was stored unless the object has a tag stored already. Returns : value of tagname (a scalar) Args : new value (a scalar, optional) Specific accessors for Tree tree_id Title : tree_id Usage : $obj->tree_id($newval) Function: Get/set a name for the tree Returns : value of tagname (a scalar) Args : new value (a scalar, optional) tree Title : tree Usage : $obj->tree($newval) Function: Get/set tree Returns : tree ref Args : new value (a tree ref, optional) perl v5.14.2 2012-03-02 Bio::Annotation::Tree(3pm)